Package pl.poznan.put.structure.formats

Class BpSeq.Entry

java.lang.Object

pl.poznan.put.structure.formats.BpSeq.Entry

All Implemented Interfaces:

Serializable, Comparable<BpSeq.Entry>

Direct Known Subclasses:

ImmutableEntry

Enclosing class:

BpSeq

@Immutable
public abstract static class BpSeq.Entry
extends Object
implements Comparable<BpSeq.Entry>, Serializable

An entry of a BPSEQ data.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
Entry()

Method Summary

Modifier and Type	Method	Description
String	comment()
int	compareTo(BpSeq.Entry t)
boolean	contains(int index)	Checks for a paired BPSEQ entry (i, j) if a given index k lies between them: i < k < j.
static BpSeq.Entry	fromString(String line)	Parses a string into a BPSEQ entry.
abstract int	index()
boolean	isPaired()
int	length()
abstract int	pair()
abstract char	seq()
String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Entry

public Entry()

Method Detail

fromString

public static BpSeq.Entry fromString(String line)

Parses a string into a BPSEQ entry. Expected format: int char int

Parameters:

line - A line containing a BPSEQ entry.

Returns:

An instance of this class.

index

@Parameter(order=1)
public abstract int index()

Returns:

The value of index column.

seq

@Parameter(order=2)
public abstract char seq()

Returns:

The value of sequence column.

pair

@Parameter(order=3)
public abstract int pair()

Returns:

The value of pair column.

comment

@Default
public String comment()

Returns:

The optional comment.

isPaired

public boolean isPaired()

Returns:

True if pair column is non-zero.

contains

public final boolean contains(int index)

Checks for a paired BPSEQ entry (i, j) if a given index k lies between them: i < k < j.

Parameters:

index - The index to check

Returns:

True if index lies between this entry and its pair.

length

public final int length()

Returns:

The difference between pair column and index column or 0 for unpaired entries.

compareTo

public final int compareTo(BpSeq.Entry t)

Specified by:

compareTo in interface Comparable<BpSeq.Entry>

toString

public String toString()

Overrides:

toString in class Object